Having worked in various Maritime Museums, I've been exposed to a great deal of trunnel lore. The Gloucester schooners, mostly built in Essex, were trunnel fastened as were most commercial wooden sailing ships.
A plank would be hung with a few spikes, say one for every two frames, then bored and trunneled, usually right through the ceiling and wedged both ends. Locust was the preferred material. No bedding, just driven dry and tight. Of course, this is in heavy sawn frames only, not light bent frames like in boat work.
The CHARLES W MORGAN's bottom planking lasted over 150 years like this. No electrolysis or other metal diseases, but yes, a path to the heart of the frame for moisture I suppose.
Here are a couple of photos from the Story yard in Essex. In the first one the fastening crew is trunneling off a plank. In the second pic of caulkers at work on a very tight seam with a line of reaming irons. If you look closely, you'll see the occasional white pine plug over a spike head, and the rest of the fasteners being locust trunnels with a wedge.
1 1/8" minimum size, up to 1 1/2" for heavy work.